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Afsari S, Mukherjee S, Halloran N, Ghirlanda G, Ryan E, Wang X, Lindsay S. Heavy Water Reduces the Electronic Conductance of Protein Wires via Deuteron Interactions with Aromatic Residues. Nano Lett 2023; 23:8907-8913. [PMID: 37772726 DOI: 10.1021/acs.nanolett.3c02263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
Proteins are versatile, self-assembling nanoelectronic components, but their hopping conductivity is expected to be influenced by solvent fluctuations. The role of the solvent was investigated by measuring the single molecule conductance of several proteins in both H2O and D2O. The conductance of a homologous series of protein wires decreases more rapidly with length in D2O, indicating a 6-fold decrease in carrier diffusion constant relative to the same protein in H2O. The effect was found to depend on the specific aromatic amino acid composition. A tryptophan zipper protein showed a decrease in conductance similar to that of the protein wires, whereas a phenylalanine zipper protein was insensitive to solvent changes. Tryptophan contains an indole amine, whereas the phenylalanine aromatic ring has no exchangeable protons, so the effect of heavy water on conductance is a consequence of specific D- or H-interactions with the aromatic residues.
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Lu J, Rahman MI, Kazan IC, Halloran NR, Bobkov AA, Ozkan SB, Ghirlanda G. Engineering gain-of-function mutants of a WW domain by dynamics and structural analysis. Protein Sci 2023; 32:e4759. [PMID: 37574787 PMCID: PMC10464296 DOI: 10.1002/pro.4759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 07/17/2023] [Accepted: 08/10/2023] [Indexed: 08/15/2023]
Abstract
Proteins gain optimal fitness such as foldability and function through evolutionary selection. However, classical studies have found that evolutionarily designed protein sequences alone cannot guarantee foldability, or at least not without considering local contacts associated with the initial folding steps. We previously showed that foldability and function can be restored by removing frustration in the folding energy landscape of a model WW domain protein, CC16, which was designed based on Statistical Coupling Analysis (SCA). Substitutions ensuring the formation of five local contacts identified as "on-path" were selected using the closest homolog native folded sequence, N21. Surprisingly, the resulting sequence, CC16-N21, bound to Group I peptides, while N21 did not. Here, we identified single-point mutations that enable N21 to bind a Group I peptide ligand through structure and dynamic-based computational design. Comparison of the docked position of the CC16-N21/ligand complex with the N21 structure showed that residues at positions 9 and 19 are important for peptide binding, whereas the dynamic profiles identified position 10 as allosterically coupled to the binding site and exhibiting different dynamics between N21 and CC16-N21. We found that swapping these positions in N21 with matched residues from CC16-N21 recovers nature-like binding affinity to N21. This study validates the use of dynamic profiles as guiding principles for affecting the binding affinity of small proteins.
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Affiliation(s)
- Jin Lu
- Department of Physics and Center for Biological PhysicsArizona State UniversityTempeArizonaUSA
| | | | - I. Can Kazan
- Department of Physics and Center for Biological PhysicsArizona State UniversityTempeArizonaUSA
| | | | - Andrey A. Bobkov
- Conrad Prebys Center for Chemical GenomicsSanford Burnham Prebys Medical Discovery InstituteCaliforniaUSA
| | - S. Banu Ozkan
- Department of Physics and Center for Biological PhysicsArizona State UniversityTempeArizonaUSA
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Carrara E, Sibani M, Barbato L, Mazzaferri F, Salerno ND, Conti M, Azzini AM, Dalbeni A, Pellizzari L, Fontana G, Di Francesco V, Bissoli L, Del Monte L, Zamboni M, Olivieri O, Minuz P, Maccacaro L, Ghirlanda G, Tacconelli E. How to 'SAVE' antibiotics: effectiveness and sustainability of a new model of antibiotic stewardship intervention in the internal medicine area. Int J Antimicrob Agents 2022; 60:106672. [PMID: 36103917 DOI: 10.1016/j.ijantimicag.2022.106672] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 08/12/2022] [Accepted: 09/09/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND Antibiotic stewardship (AS) is a cornerstone of the fight against antimicrobial resistance; however, evidence on the best practice to improve antibiotic prescription in various hospital settings is still scarce. This study aimed to measure the efficacy of a non-restrictive AS intervention in the internal medicine area of a tertiary-care hospital across a 3-year period. METHODS The intervention comprised a 3-month 'intensive phase' based on education and guidelines provision, followed by 9 months of audits and feedback activities. The primary outcome was the overall antibiotic consumption measured as days of therapy (DOTs) and defined daily doses (DDDs). Secondary outcomes were carbapenem and fluoroquinolone consumption, all-cause in-hospital mortality, length of stay, incidence of Clostridioides difficile and carbapenem-resistant Enterobacterales bloodstream infections (CRE-BSIs). All outcomes were measured in the intervention wards comparing the pre-phase with the post-phase using an interrupted time-series model. RESULTS A total of 145 337 patient days (PDs) and 14 159 admissions were included in the analysis. The intervention was associated with reduced DOTs*1000PDs (-162.2/P = 0.005) and DDDs*1000PDs (-183.6/P ≤ 0.001). A sustained decrease in ward-related antibiotic consumption was also detected during the post-intervention phase and in the carbapenem/fluoroquinolone classes. The intervention was associated with an immediate reduction in length of stay (-1.72 days/P < 0.001) and all-cause mortality (-3.71 deaths*100 admissions/P = 0.002), with a decreasing trend over time. Rates of Clostridioides difficile infections and CRE-BSIs were not significantly impacted by the intervention. CONCLUSIONS The AS intervention was effective and safe in decreasing antibiotic consumption and length of stay in the internal medicine area. Enabling prescribers to judicious use of antimicrobials through active participation in AS initiatives is key to reach sustained results over time.
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Affiliation(s)
- Elena Carrara
- Division of Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, Italy.
| | - Marcella Sibani
- Division of Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, Italy; Infectious Diseases Department, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Lorenzo Barbato
- Department of Pharmacy, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Fulvia Mazzaferri
- Infectious Diseases Department, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Nicola Duccio Salerno
- Division of Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, Italy
| | - Michela Conti
- Division of Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, Italy
| | - Anna Maria Azzini
- Division of Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, Italy
| | - Andrea Dalbeni
- Department of Medicine, General Medicine C Unit & Liver Unit, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Luca Pellizzari
- Geriatric Unit A, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Giorgia Fontana
- Geriatric Unit A, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | | | - Luisa Bissoli
- Department of Medicine, Section of Geriatrics, University of Verona, Verona, Italy
| | - Letizia Del Monte
- Department of Medicine, Section of Geriatrics, University of Verona, Verona, Italy
| | - Mauro Zamboni
- Department of Medicine, Section of Geriatrics, University of Verona, Verona, Italy
| | - Oliviero Olivieri
- Medicina Interna ad Indirizzo Immunoematologico ed Emocoagulativo, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Pietro Minuz
- Department of Medicine, Section of General Medicine and Hypertension, University of Verona, Verona, Italy
| | - Laura Maccacaro
- Unit of Microbiology and Virology, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Giovanna Ghirlanda
- Medical Direction, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Evelina Tacconelli
- Division of Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, Italy
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Kazan IC, Sharma P, Rahman MI, Bobkov A, Fromme R, Ghirlanda G, Ozkan SB. Design of novel cyanovirin-N variants by modulation of binding dynamics through distal mutations. eLife 2022; 11:67474. [PMID: 36472898 PMCID: PMC9725752 DOI: 10.7554/elife.67474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 11/28/2022] [Indexed: 12/07/2022] Open
Abstract
We develop integrated co-evolution and dynamic coupling (ICDC) approach to identify, mutate, and assess distal sites to modulate function. We validate the approach first by analyzing the existing mutational fitness data of TEM-1 β-lactamase and show that allosteric positions co-evolved and dynamically coupled with the active site significantly modulate function. We further apply ICDC approach to identify positions and their mutations that can modulate binding affinity in a lectin, cyanovirin-N (CV-N), that selectively binds to dimannose, and predict binding energies of its variants through Adaptive BP-Dock. Computational and experimental analyses reveal that binding enhancing mutants identified by ICDC impact the dynamics of the binding pocket, and show that rigidification of the binding residues compensates for the entropic cost of binding. This work suggests a mechanism by which distal mutations modulate function through dynamic allostery and provides a blueprint to identify candidates for mutagenesis in order to optimize protein function.
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Affiliation(s)
- I Can Kazan
- Center for Biological Physics and Department of Physics, Arizona State UniversityTempeUnited States,School of Molecular Sciences, Arizona State UniversityTempeUnited States
| | - Prerna Sharma
- School of Molecular Sciences, Arizona State UniversityTempeUnited States
| | | | - Andrey Bobkov
- Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
| | - Raimund Fromme
- School of Molecular Sciences, Arizona State UniversityTempeUnited States
| | - Giovanna Ghirlanda
- School of Molecular Sciences, Arizona State UniversityTempeUnited States
| | - S Banu Ozkan
- Center for Biological Physics and Department of Physics, Arizona State UniversityTempeUnited States
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Rosati P, Basa S, Blain AW, Bozzo E, Branchesi M, Christensen L, Ferrara A, Gomboc A, O’Brien PT, Osborne JP, Rossi A, Schüssler F, Spurio M, Stergioulas N, Stratta G, Amati L, Casewell S, Ciolfi R, Ghirlanda G, Grimm S, Guetta D, Harms J, Le Floc’h E, Longo F, Maggiore M, Mereghetti S, Oganesyan G, Salvaterra R, Tanvir NR, Turriziani S, Vergani SD, Balman S, Caruana J, Erkut MH, Guidorzi G, Frontera F, Martin-Carrillo A, Paltani S, Porquet D, Sergijenko O. Synergies of THESEUS with the large facilities of the 2030s and guest observer opportunities. Exp Astron (Dordr) 2021; 52:407-437. [PMID: 35153378 PMCID: PMC8807471 DOI: 10.1007/s10686-021-09764-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 05/12/2021] [Indexed: 06/14/2023]
Abstract
The proposed THESEUS mission will vastly expand the capabilities to monitor the high-energy sky. It will specifically exploit large samples of gamma-ray bursts to probe the early universe back to the first generation of stars, and to advance multi-messenger astrophysics by detecting and localizing the counterparts of gravitational waves and cosmic neutrino sources. The combination and coordination of these activities with multi-wavelength, multi-messenger facilities expected to be operating in the 2030s will open new avenues of exploration in many areas of astrophysics, cosmology and fundamental physics, thus adding considerable strength to the overall scientific impact of THESEUS and these facilities. We discuss here a number of these powerful synergies and guest observer opportunities.
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Affiliation(s)
- P. Rosati
- Department of Physics and Earth Sciences, University of Ferrara, Via G. Saragat, 1, 44122 Ferrara, Italy
| | - S. Basa
- Aix Marseille University, CNRS, CNES, LAM, Marseille, France
| | - A. W. Blain
- School of Physics and Astronomy, University of Leicester, University Road, Leicester, LE1 7RH UK
| | - E. Bozzo
- Department of Astronomy, University of Geneva, Chemin d’Ecogia 16, CH-1290 Versoix, Switzerland
| | - M. Branchesi
- Gran Sasso Science Institute, Viale F. Crispi 7, 67100 L’Aquila, AQ Italy
- INFN, Laboratori Nazionali del Gran Sasso, 67100 Assergi, Italy
| | - L. Christensen
- Niels Bohr Institute, University of Copenhagen, Jagtvej 128, 2200 Copenhagen N, Denmark
| | - A. Ferrara
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - A. Gomboc
- Center for Astrophysics and Cosmology, University of Nova Gorica, Vipavska 13, 5000 Nova Gorica, Slovenia
| | - P. T. O’Brien
- School of Physics and Astronomy, University of Leicester, University Road, Leicester, LE1 7RH UK
| | - J. P. Osborne
- School of Physics and Astronomy, University of Leicester, University Road, Leicester, LE1 7RH UK
| | - A. Rossi
- INAF, Osservatorio di Astrofisica e Scienza dello Spazio, via Piero Gobetti 93/3, 40129 Bologna, Italy
| | - F. Schüssler
- IRFU, CEA, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - M. Spurio
- Dipartimento di Fisica e Astronomia dell’Università, Viale Berti Pichat 6/2, 40127 Bologna, Italy
- INFN - Sezione di Bologna, Viale Berti-Pichat 6/2, 40127 Bologna, Italy
| | - N. Stergioulas
- Department of Physics, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - G. Stratta
- INAF, Osservatorio di Astrofisica e Scienza dello Spazio, via Piero Gobetti 93/3, 40129 Bologna, Italy
| | - L. Amati
- INAF, Osservatorio di Astrofisica e Scienza dello Spazio, via Piero Gobetti 93/3, 40129 Bologna, Italy
| | - S. Casewell
- School of Physics and Astronomy, University of Leicester, University Road, Leicester, LE1 7RH UK
| | - R. Ciolfi
- INAF, Osservatorio Astronomico di Padova, Vicolo dell’Osservatorio 5, 35122 Padova, Italy
| | - G. Ghirlanda
- INAF, Osservatorio Astronomico di Brera, Via Bianchi 46, 23807 Merate, LC Italy
| | - S. Grimm
- Gran Sasso Science Institute, Viale F. Crispi 7, 67100 L’Aquila, AQ Italy
- INFN, Laboratori Nazionali del Gran Sasso, 67100 Assergi, Italy
| | - D. Guetta
- ORT Braude, Karmiel, Israel
- Physics Department, University of Ariel, Ariel, West Bank, Israel
| | - J. Harms
- Gran Sasso Science Institute, Viale F. Crispi 7, 67100 L’Aquila, AQ Italy
- INFN, Laboratori Nazionali del Gran Sasso, 67100 Assergi, Italy
| | - E. Le Floc’h
- AIM, CEA-Irfu/DAp, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - F. Longo
- Dipartimento di Fisica, Università degli Studi di Trieste and Istituto Nazionale di Fisica Nucleare, Sezione di Trieste, via Valerio 2, 34127 Trieste, Italy
| | - M. Maggiore
- Départment de Physique Théorique and Center for Astroparticle Physics, Université de Genève, 24 quai Ansermet, CH–1211 Genève 4, Switzerland
| | - S. Mereghetti
- INAF, Istituto di Astrofisica Spaziale e Fisica Cosmica, via Alfonso Corti 12, 20133 Milano, Italy
| | - G. Oganesyan
- Gran Sasso Science Institute, Viale F. Crispi 7, 67100 L’Aquila, AQ Italy
- INFN, Laboratori Nazionali del Gran Sasso, 67100 Assergi, Italy
| | - R. Salvaterra
- INAF, Istituto di Astrofisica Spaziale e Fisica Cosmica, via Alfonso Corti 12, 20133 Milano, Italy
| | - N. R. Tanvir
- School of Physics and Astronomy, University of Leicester, University Road, Leicester, LE1 7RH UK
| | - S. Turriziani
- Physics Department, Gubkin Russian State University, 65 Leninsky Prospekt, Moscow, 119991 Russian Federation
| | - S. D. Vergani
- GEPI, Observatoire de Paris, PSL University, CNRS, Place Jules Janssen, 92190 Meudon, France
| | - S. Balman
- Department of Astronomy and Space Sciences, Istanbul University, Faculty of Science, Beyazit, 34119 Istanbul, Turkey
| | - J. Caruana
- Department of Physics and Institute of Space Sciences and Astronomy, University of Malta, Msida, MSD 2080 Malta
| | - M. H. Erkut
- Faculty of Engineering and Natural Sciences, Istanbul Bilgi University, 34060 Istanbul, Turkey
| | - G. Guidorzi
- Department of Physics and Earth Sciences, University of Ferrara, Via G. Saragat, 1, 44122 Ferrara, Italy
| | - F. Frontera
- Department of Physics and Earth Sciences, University of Ferrara, Via G. Saragat, 1, 44122 Ferrara, Italy
| | - A. Martin-Carrillo
- School of Physics and Centre for Space Research, University College Dublin, Dublin 4, Ireland
| | - S. Paltani
- Department of Astronomy, University of Geneva, Chemin d’Ecogia 16, CH-1290 Versoix, Switzerland
| | - D. Porquet
- Aix Marseille University, CNRS, CNES, LAM, Marseille, France
| | - O. Sergijenko
- Astronomical Observatory of Taras Shevchenko National University of Kyiv, Observatorna str., 3, Kyiv, 04053 Ukraine
- Main Astronomical Observatory of the National Academy of Sciences of Ukraine, Zabolotnoho str., 27, Kyiv, 03680 Ukraine
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Porru S, Monaco MGL, Carta A, Spiteri G, Parpaiola M, Battaggia A, Galligioni G, Ferrazzi B, Lo Cascio G, Gibellini D, Peretti A, Brutti M, Tardivo S, Ghirlanda G, Verlato G, Gaino S, Peserico D, Bassi A, Lippi G. SARS-CoV-2 Infection in Health Workers: Analysis from Verona SIEROEPID Study during the Pre-Vaccination Era. Int J Environ Res Public Health 2021; 18:ijerph18126446. [PMID: 34198715 PMCID: PMC8296263 DOI: 10.3390/ijerph18126446] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 06/10/2021] [Accepted: 06/10/2021] [Indexed: 12/24/2022]
Abstract
Background: To report the baseline phase of the SIEROEPID study on SARS-CoV-2 infection seroprevalence among health workers at the University Hospital of Verona, Italy, between spring and fall 2020; to compare performances of several laboratory tests for SARS-CoV-2 antibody detection. Methods: 5299 voluntary health workers were enrolled from 28 April 2020 to 28 July 2020 to assess immunological response to SARS-CoV-2 infection throughout IgM, IgG and IgA serum levels titration by four laboratory tests. Association of antibody titre with several demographic variables, swab tests and performance tests (sensitivity, specificity, and agreement) were statistically analyzed. Results: The overall seroprevalence was 6%, considering either IgG and IgM, and 4.8% considering IgG. Working in COVID-19 Units was not associated with a statistically significant increase in the number of infected workers. Cohen’s kappa of agreement between MaglumiTM and VivaDiagTM was quite good when considering IgG only (Cohen’s kappa = 78.1%, 95% CI 74.0–82.0%), but was lower considering IgM (Cohen’s kappa = 13.3%, 95% CI 7.8–18.7%). Conclusion: The large sample size with high participation (84.7%), the biobank and the longitudinal design were significant achievements, offering a baseline dataset as the benchmark for risk assessment, health surveillance and management of SARS-CoV-2 infection for the hospital workforce, especially considering the ongoing vaccination campaign. Study results support the national regulator guidelines on using swabs for SARS-CoV-2 screening with health workers and using the serological tests to contribute to the epidemiological assessment of the spread of the virus.
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Affiliation(s)
- Stefano Porru
- Section of Occupational Medicine, Department of Diagnostics and Public Health, University of Verona, 37134 Verona, Italy; (S.P.); (A.C.)
- Clinical Unit of Occupational Medicine, University Hospital of Verona, 37134 Verona, Italy;
| | - Maria Grazia Lourdes Monaco
- Clinical Unit of Occupational Medicine, University Hospital of Verona, 37134 Verona, Italy;
- Correspondence: ; Tel.: +0039-0458123946
| | - Angela Carta
- Section of Occupational Medicine, Department of Diagnostics and Public Health, University of Verona, 37134 Verona, Italy; (S.P.); (A.C.)
- Clinical Unit of Occupational Medicine, University Hospital of Verona, 37134 Verona, Italy;
| | - Gianluca Spiteri
- Clinical Unit of Occupational Medicine, University Hospital of Verona, 37134 Verona, Italy;
| | - Marco Parpaiola
- Postgraduate School of Occupational Medicine, University of Verona, 37134 Verona, Italy; (M.P.); (A.B.); (G.G.); (B.F.)
| | - Andrea Battaggia
- Postgraduate School of Occupational Medicine, University of Verona, 37134 Verona, Italy; (M.P.); (A.B.); (G.G.); (B.F.)
| | - Giulia Galligioni
- Postgraduate School of Occupational Medicine, University of Verona, 37134 Verona, Italy; (M.P.); (A.B.); (G.G.); (B.F.)
| | - Beatrice Ferrazzi
- Postgraduate School of Occupational Medicine, University of Verona, 37134 Verona, Italy; (M.P.); (A.B.); (G.G.); (B.F.)
| | | | - Davide Gibellini
- Section of Microbiology, Department of Diagnostics and Public Health, University of Verona, 37134 Verona, Italy;
- Unit of Microbiology and Virology, University Hospital of Verona, 37134 Verona, Italy; (A.P.); (M.B.)
| | - Angelo Peretti
- Unit of Microbiology and Virology, University Hospital of Verona, 37134 Verona, Italy; (A.P.); (M.B.)
| | - Martina Brutti
- Unit of Microbiology and Virology, University Hospital of Verona, 37134 Verona, Italy; (A.P.); (M.B.)
| | - Stefano Tardivo
- Section of Hygiene, Department of Diagnostics and Public Health, University of Verona, 37134 Verona, Italy;
| | | | - Giuseppe Verlato
- Unit of Epidemiology and Medical Statistics, Department of Diagnostics and Public Health, University of Verona, 37134 Verona, Italy;
| | - Stefania Gaino
- Laboratory of Clinical Chemistry and Hematology, University Hospital of Verona, 37134 Verona, Italy; (S.G.); (A.B.); (G.L.)
- Section of Clinical Biochemistry, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy;
| | - Denise Peserico
- Section of Clinical Biochemistry, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy;
| | - Antonella Bassi
- Laboratory of Clinical Chemistry and Hematology, University Hospital of Verona, 37134 Verona, Italy; (S.G.); (A.B.); (G.L.)
- Section of Clinical Biochemistry, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy;
| | - Giuseppe Lippi
- Laboratory of Clinical Chemistry and Hematology, University Hospital of Verona, 37134 Verona, Italy; (S.G.); (A.B.); (G.L.)
- Section of Clinical Biochemistry, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy;
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Alcala-Torano R, Halloran N, Gwerder N, Sommer DJ, Ghirlanda G. Light-Driven CO 2 Reduction by Co-Cytochrome b 562. Front Mol Biosci 2021; 8:609654. [PMID: 33937320 PMCID: PMC8082397 DOI: 10.3389/fmolb.2021.609654] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 01/11/2021] [Indexed: 11/23/2022] Open
Abstract
The current trend in atmospheric carbon dioxide concentrations is causing increasing concerns for its environmental impacts, and spurring the developments of sustainable methods to reduce CO2 to usable molecules. We report the light-driven CO2 reduction in water in mild conditions by artificial protein catalysts based on cytochrome b 562 and incorporating cobalt protoporphyrin IX as cofactor. Incorporation into the protein scaffolds enhances the intrinsic reactivity of the cobalt porphyrin toward proton reduction and CO generation. Mutations around the binding site modulate the activity of the enzyme, pointing to the possibility of further improving catalytic activity through rational design or directed evolution.
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Affiliation(s)
| | | | | | | | - Giovanna Ghirlanda
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States
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Zou T, Woodrum BW, Halloran N, Campitelli P, Bobkov AA, Ghirlanda G, Ozkan SB. Local Interactions That Contribute Minimal Frustration Determine Foldability. J Phys Chem B 2021; 125:2617-2626. [PMID: 33687216 DOI: 10.1021/acs.jpcb.1c00364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Earlier experiments suggest that the evolutionary information (conservation and coevolution) encoded in protein sequences is necessary and sufficient to specify the fold of a protein family. However, there is no computational work to quantify the effect of such evolutionary information on the folding process. Here we explore the role of early folding steps for sequences designed using coevolution and conservation through a combination of computational and experimental methods. We simulated a repertoire of native and designed WW domain sequences to analyze early local contact formation and found that the N-terminal β-hairpin turn would not form correctly due to strong non-native local contacts in unfoldable sequences. Through a maximum likelihood approach, we identified five local contacts that play a critical role in folding, suggesting that a small subset of amino acid pairs can be used to solve the "needle in the haystack" problem to design foldable sequences. Thus, using the contact probability of those five local contacts that form during the early stage of folding, we built a classification model that predicts the foldability of a WW sequence with 81% accuracy. This classification model was used to redesign WW domain sequences that could not fold due to frustration and make them foldable by introducing a few mutations that led to the stabilization of these critical local contacts. The experimental analysis shows that a redesigned sequence folds and binds to polyproline peptides with a similar affinity as those observed for native WW domains. Overall, our analysis shows that evolutionary-designed sequences should not only satisfy the folding stability but also ensure a minimally frustrated folding landscape.
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Affiliation(s)
- Taisong Zou
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona 85287, United States
| | - Brian W Woodrum
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Nicholas Halloran
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Paul Campitelli
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona 85287, United States
| | - Andrey A Bobkov
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Giovanna Ghirlanda
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Sefika Banu Ozkan
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona 85287, United States
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Roy A, Vaughn MD, Tomlin J, Booher GJ, Kodis G, Simmons CR, Allen JP, Ghirlanda G. Enhanced Photocatalytic Hydrogen Production by Hybrid Streptavidin-Diiron Catalysts. Chemistry 2020; 26:6240-6246. [PMID: 32201996 DOI: 10.1002/chem.202000204] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/24/2020] [Indexed: 01/22/2023]
Abstract
Hybrid protein-organometallic catalysts are being explored for selective catalysis of a number of reactions, because they utilize the complementary strengths of proteins and of organometallic complex. Herein, we present an artificial hydrogenase, StrepH2, built by incorporating a biotinylated [Fe-Fe] hydrogenase organometallic mimic within streptavidin. This strategy takes advantage of the remarkable strength and specificity of biotin-streptavidin recognition, which drives quantitative incorporation of the biotinylated diironhexacarbonyl center into streptavidin, as confirmed by UV/Vis spectroscopy and X-ray crystallography. FTIR spectra of StrepH2 show characteristic peaks at shift values indicative of interactions between the catalyst and the protein scaffold. StrepH2 catalyzes proton reduction to hydrogen in aqueous media during photo- and electrocatalysis. Under photocatalytic conditions, the protein-embedded catalyst shows enhanced efficiency and prolonged activity compared to the isolated catalyst. Transient absorption spectroscopy data suggest a mechanism for the observed increase in activity underpinned by an observed longer lifetime for the catalytic species FeI Fe0 when incorporated within streptavidin compared to the biotinylated catalyst in solution.
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Affiliation(s)
- Anindya Roy
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.,Present Address: Molecular Engineering and Sciences, Institute for Protein Design, University of Washington, Seattle, WA, 98195-1655, USA
| | - Michael D Vaughn
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - John Tomlin
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Garrett J Booher
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Gerdenis Kodis
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Chad R Simmons
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - James P Allen
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Giovanna Ghirlanda
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
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10
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Dong M, Harikumar KG, Raval SR, Milburn JE, Clark C, Alcala-Torano R, Mobarec JC, Reynolds CA, Ghirlanda G, Christopoulos A, Wootten D, Sexton PM, Miller LJ. Rational development of a high-affinity secretin receptor antagonist. Biochem Pharmacol 2020; 177:113929. [PMID: 32217097 DOI: 10.1016/j.bcp.2020.113929] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/19/2020] [Indexed: 01/11/2023]
Abstract
The secretin receptor is a prototypic class B GPCR with substantial and broad pharmacologic importance. The aim of this project was to develop a high affinity selective antagonist as a new and important pharmacologic tool and to aid stabilization of this receptor in an inactive conformation for ultimate structural characterization. Amino-terminal truncation of the natural 27-residue ligand reduced biological activity, but also markedly reduced binding affinity. This was rationally and experimentally overcome with lactam stabilization of helical structure and with replacement of residues with natural and unnatural amino acids. A key new step in this effort was the replacement of peptide residue Leu22 with L-cyclohexylalanine (Cha) to enhance potential hydrophobic interactions with receptor residues Leu31, Val34, and Phe92 that were predicted from molecular modeling. Alanine-replacement mutagenesis of these residues markedly affected ligand binding and biological activity. The optimal antagonist ligand, (Y10,c[E16,K20],I17,Cha22,R25)sec(6-27), exhibited high binding affinity (4 nM), similar to natural secretin, and exhibited no demonstrable biological activity to stimulate cAMP accumulation, intracellular calcium mobilization, or β-arrestin-2 translocation. It acts as an orthosteric competitive antagonist, predicted to bind within the peptide-binding groove in the receptor extracellular domain. The analogous peptide that was one residue longer, retaining Thr5, exhibited partial agonist activity, while further truncation of even a single residue (Phe6) reduced binding affinity. This sec(6-27)-based peptide will be an important new tool for pharmacological and structural studies.
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Affiliation(s)
- Maoqing Dong
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, AZ 85259, United States
| | - Kaleeckal G Harikumar
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, AZ 85259, United States
| | - Sweta R Raval
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, AZ 85259, United States
| | - Juliana E Milburn
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, AZ 85259, United States
| | - Carolyn Clark
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, United States
| | - Rafael Alcala-Torano
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, United States
| | - Juan C Mobarec
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Christopher A Reynolds
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Giovanna Ghirlanda
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, United States
| | - Arthur Christopoulos
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, 3052 Victoria, Australia
| | - Denise Wootten
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, 3052 Victoria, Australia
| | - Patrick M Sexton
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, 3052 Victoria, Australia
| | - Laurence J Miller
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, AZ 85259, United States.
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11
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Costantino M, Sharma P, Vaiana SM, Ghirlanda G. Liquid-Liquid Phase Separation of Intrinsically Disordered Proteins for Development of Membraneless Organelles in Synthetic Cells. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.1269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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12
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Pattni V, Vaiana SM, Ghirlanda G, Heyden M. Modeling Liquid-Liquid Phase Separations of Intrinsically Disordered Proteins on the Micrometer-Scale. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.2962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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13
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Call A, Casadevall C, Romero-Rivera A, Martin-Diaconescu V, Sommer DJ, Osuna S, Ghirlanda G, Lloret-Fillol J. Improved Electro- and Photocatalytic Water Reduction by Confined Cobalt Catalysts in Streptavidin. ACS Catal 2019. [DOI: 10.1021/acscatal.8b04981] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Arnau Call
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Avinguda Països Catalans 16, 43007 Tarragona, Spain
| | - Carla Casadevall
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Avinguda Països Catalans 16, 43007 Tarragona, Spain
| | - Adrian Romero-Rivera
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain
| | - Vlad Martin-Diaconescu
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Avinguda Països Catalans 16, 43007 Tarragona, Spain
| | - Dayn J. Sommer
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluïs Companys, 23, 08010, Barcelona, Spain
| | - Giovanna Ghirlanda
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Julio Lloret-Fillol
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Avinguda Països Catalans 16, 43007 Tarragona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluïs Companys, 23, 08010, Barcelona, Spain
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14
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Mejias SH, Bahrami-Dizicheh Z, Liutkus M, Sommer DJ, Astashkin A, Kodis G, Ghirlanda G, Cortajarena AL. Repeat proteins as versatile scaffolds for arrays of redox-active FeS clusters. Chem Commun (Camb) 2019; 55:3319-3322. [PMID: 30829362 PMCID: PMC6484676 DOI: 10.1039/c8cc06827e] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Molecular string of beads: modular extension of a protein backbone builds a chain of electroactive clusters.
Arrays of one, two and four electron-transfer active [4Fe–4S] clusters were constructed on modular tetratricopeptide repeat protein scaffolds, with the number of clusters determined solely by the size of the scaffold. The constructs show reversible redox activity and transient charge stabilization necessary to facilitate charge transfer.
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Affiliation(s)
- Sara H Mejias
- CIC biomaGUNE Paseo de Miramón 182, E-20014 Donostia-San Sebastian, Spain
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15
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Ghirlanda G, Salafia OS, Paragi Z, Giroletti M, Yang J, Marcote B, Blanchard J, Agudo I, An T, Bernardini MG, Beswick R, Branchesi M, Campana S, Casadio C, Chassande-Mottin E, Colpi M, Covino S, D'Avanzo P, D'Elia V, Frey S, Gawronski M, Ghisellini G, Gurvits LI, Jonker PG, van Langevelde HJ, Melandri A, Moldon J, Nava L, Perego A, Perez-Torres MA, Reynolds C, Salvaterra R, Tagliaferri G, Venturi T, Vergani SD, Zhang M. Compact radio emission indicates a structured jet was produced by a binary neutron star merger. Science 2019; 363:968-971. [PMID: 30792360 DOI: 10.1126/science.aau8815] [Citation(s) in RCA: 197] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 02/06/2019] [Indexed: 11/02/2022]
Abstract
The binary neutron star merger event GW170817 was detected through both electromagnetic radiation and gravitational waves. Its afterglow emission may have been produced by either a narrow relativistic jet or an isotropic outflow. High-spatial-resolution measurements of the source size and displacement can discriminate between these scenarios. We present very-long-baseline interferometry observations, performed 207.4 days after the merger by using a global network of 32 radio telescopes. The apparent source size is constrained to be smaller than 2.5 milli-arc seconds at the 90% confidence level. This excludes the isotropic outflow scenario, which would have produced a larger apparent size, indicating that GW170817 produced a structured relativistic jet. Our rate calculations show that at least 10% of neutron star mergers produce such a jet.
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Affiliation(s)
- G Ghirlanda
- Istituto Nazionale di Astrofisica-Osservatorio Astronomico di Brera, Via E. Bianchi 46, I-23807 Merate, Italy. .,Dipartimento di Fisica G. Occhialini, Università di Milano-Bicocca, Piazza della Scienza 3, IT-20126 Milano, Italy.,Sezione di Milano Bicocca, Istituto Nazionale Fisica Nucleare (INFN), Piazza della Scienza 3, 20126 Milano, Italy
| | - O S Salafia
- Istituto Nazionale di Astrofisica-Osservatorio Astronomico di Brera, Via E. Bianchi 46, I-23807 Merate, Italy. .,Dipartimento di Fisica G. Occhialini, Università di Milano-Bicocca, Piazza della Scienza 3, IT-20126 Milano, Italy.,Sezione di Milano Bicocca, Istituto Nazionale Fisica Nucleare (INFN), Piazza della Scienza 3, 20126 Milano, Italy
| | - Z Paragi
- Joint Institute for Very Long Baseline Interferometry (VLBI) European Research Infrastructure Consortium (ERIC), Oude Hoogeveensedijk 4, 7991 PD Dwingeloo, Netherlands
| | - M Giroletti
- Istituto Nazionale di Astrofisica-Istituto di Radioastronomia, via Gobetti 101, I40129, Bologna, Italia
| | - J Yang
- Chalmers University of Technology, Onsala Space Observatory, SE-439 92, Sweden.,Yunnan Observatories, Chinese Academy of Sciences, 650216 Kunming, Yunnan, China
| | - B Marcote
- Joint Institute for Very Long Baseline Interferometry (VLBI) European Research Infrastructure Consortium (ERIC), Oude Hoogeveensedijk 4, 7991 PD Dwingeloo, Netherlands
| | - J Blanchard
- Joint Institute for Very Long Baseline Interferometry (VLBI) European Research Infrastructure Consortium (ERIC), Oude Hoogeveensedijk 4, 7991 PD Dwingeloo, Netherlands
| | - I Agudo
- Instituto de Astrofísica de Andalucía-Consejo Superior de Investigaciones Científicas (CSIC), Glorieta de la Astronomía s/n, E-18008, Granada, Spain
| | - T An
- Shanghai Astronomical Observatory, Key Laboratory of Radio Astronomy, Chinese Academy of Sciences, 200030 Shanghai, China
| | - M G Bernardini
- Laboratoire Univers et Particules de Montpellier, Universitè de Montpellier, Centre National de la Recherche Scientifique/Institute National de Physique Nucleaire et Physique des Particules (CNRS/IN2P3), place Eugéne Bataillon, F-34085 Montpellier, France
| | - R Beswick
- Electronic Multi-Element Radio Linked Interferometer Network/Very Long Baseline Interferometry (e-MERLIN/VLBI) National Facility, Jodrell Bank Centre for Astrophysics, School of Physics and Astronomy, University of Manchester, Manchester, UK
| | - M Branchesi
- Gran Sasso Science Institute, Viale F. Crispi 7, I-67100, L'Aquila, Italy.,Laboratori Nazionali del Gran Sasso, INFN, I-67100 L'Aquila, Italy
| | - S Campana
- Istituto Nazionale di Astrofisica-Osservatorio Astronomico di Brera, Via E. Bianchi 46, I-23807 Merate, Italy
| | - C Casadio
- Max Planck Institute fur Radioastronomie, Auf dem Huegel 69, Bonn D-53121, Germany
| | - E Chassande-Mottin
- AstroParticule et Cosmologie (APC), Université Paris Diderot, CNRS/IN2P3, Commissariat à l'Énergie Atomique et aux Énergies Alternatives/ Institute for Research on the Fundamental Laws of the Universe (CEA/IRFU), Observatoire de Paris, Sorbonne Paris Cité, F-75205 Paris Cedex 13, France
| | - M Colpi
- Dipartimento di Fisica G. Occhialini, Università di Milano-Bicocca, Piazza della Scienza 3, IT-20126 Milano, Italy.,Sezione di Milano Bicocca, Istituto Nazionale Fisica Nucleare (INFN), Piazza della Scienza 3, 20126 Milano, Italy
| | - S Covino
- Istituto Nazionale di Astrofisica-Osservatorio Astronomico di Brera, Via E. Bianchi 46, I-23807 Merate, Italy
| | - P D'Avanzo
- Istituto Nazionale di Astrofisica-Osservatorio Astronomico di Brera, Via E. Bianchi 46, I-23807 Merate, Italy
| | - V D'Elia
- Space Science Data Center, Agenzia Spaziale Italiana (ASI), Via del Politecnico, 00133, Roma, Italy
| | - S Frey
- Konkoly Observatory, Magyar Tudományos Akadémia (MTA) Research Centre for Astronomy and Earth Sciences, Konkoly Thege Miklós út 15-17, H-1121 Budapest, Hungary
| | - M Gawronski
- Centre for Astronomy, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Torun, Poland
| | - G Ghisellini
- Istituto Nazionale di Astrofisica-Osservatorio Astronomico di Brera, Via E. Bianchi 46, I-23807 Merate, Italy
| | - L I Gurvits
- Joint Institute for Very Long Baseline Interferometry (VLBI) European Research Infrastructure Consortium (ERIC), Oude Hoogeveensedijk 4, 7991 PD Dwingeloo, Netherlands.,Department of Astrodynamics and Space Missions, Delft University of Technology, Kluyverweg 1, 2629 HS Delft, Netherlands
| | - P G Jonker
- Space Research Organisation of the Netherlands (SRON), Netherlands Institute for Space Research, Sorbonnelaan 2, 3584 CA Utrecht, Netherlands.,Department of Astrophysics, Institute for Mathematics, Astrophysics and Particle Physics (IMAPP), Radboud University, Post Office Box 9010, 6500 GL Nijmegen, Netherlands
| | - H J van Langevelde
- Joint Institute for Very Long Baseline Interferometry (VLBI) European Research Infrastructure Consortium (ERIC), Oude Hoogeveensedijk 4, 7991 PD Dwingeloo, Netherlands.,Sterrewacht Leiden, Leiden University, Post Office Box 9513, NL-2300 RA Leiden, Netherlands
| | - A Melandri
- Istituto Nazionale di Astrofisica-Osservatorio Astronomico di Brera, Via E. Bianchi 46, I-23807 Merate, Italy
| | - J Moldon
- Electronic Multi-Element Radio Linked Interferometer Network/Very Long Baseline Interferometry (e-MERLIN/VLBI) National Facility, Jodrell Bank Centre for Astrophysics, School of Physics and Astronomy, University of Manchester, Manchester, UK
| | - L Nava
- Istituto Nazionale di Astrofisica-Osservatorio Astronomico di Brera, Via E. Bianchi 46, I-23807 Merate, Italy
| | - A Perego
- Sezione di Milano Bicocca, Istituto Nazionale Fisica Nucleare (INFN), Piazza della Scienza 3, 20126 Milano, Italy
| | - M A Perez-Torres
- Instituto de Astrofísica de Andalucía-Consejo Superior de Investigaciones Científicas (CSIC), Glorieta de la Astronomía s/n, E-18008, Granada, Spain.,Departamento de Física Teórica, Facultad de Ciencias, Universidad de Zaragoza, E-50019, Spain
| | - C Reynolds
- Commonwealth Scientific and Industrial Research Organization (CSIRO) Astronomy and Space Science, PO Box 1130, Bentley WA 6102, Australia
| | - R Salvaterra
- Istituto Nazionale di Astrofisica, Istituto di Astrofisica Spaziale e Fisica cosmica (IASF), via E. Bassini 15, 20133 Milano, Italy
| | - G Tagliaferri
- Istituto Nazionale di Astrofisica-Osservatorio Astronomico di Brera, Via E. Bianchi 46, I-23807 Merate, Italy
| | - T Venturi
- Istituto Nazionale di Astrofisica-Istituto di Radioastronomia, via Gobetti 101, I40129, Bologna, Italia
| | - S D Vergani
- Galaxies, Etoiles, Physique et Instrumentation (GEPI) Observatoire de Paris, CNRS UMR 8111, Meudon, France
| | - M Zhang
- Xinjiang Astronomical Observatory, Chinese Academy of Sciences, 150 Science 1-Street, Urumqi 831001, China.,Key Laboratory for Radio Astronomy, Chinese Academy of Sciences, 2 West Beijing Road, Nanjing 210008, China
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16
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Carli A, Moretti F, Giovanazzi G, Niero V, Perilli V, Ghirlanda G, Bovo C, Tardivo S. "Should I stay or Should I go": patient who leave Emergency Department of an Italian Third-Level Teaching Hospital. Acta Biomed 2018; 89:430-436. [PMID: 30333450 PMCID: PMC6502131 DOI: 10.23750/abm.v89i3.7596] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 08/08/2018] [Indexed: 11/23/2022]
Abstract
Background and Aim: Patients could leave ED not receiving the desired care either Without Being Seen by a doctor (LWBS) or Against Medical Advice (DAMA). In term of care quality, LWBS may be related to inappropriate access and process of care, while DAMA may lead to increased risk of mortality and re-admissions. This study aims to identify frequency of patients who leave ED, determine their characteristics and identify associated factor. Methods: This was a retrospective observational study of patients that attended EDs of University Hospital Trust of Verona in 2017. Demographic and ED access associated variables were collected for LWBS, DAMA and completed-ED-treatment patients. Univariate and multivariate data analyses was based on EMUR-PS administrative data.Results: 5,901 of 127,180 ED accesses were uncompleted treatment (4.64%); LWBS were 4,664 (79.04%) and DAMA 1,237 (20.96%). Those who leave ED tended to be younger (39.35 vs. 45.56, p<0.01). Independent factors associated with ED leaving resulted: i) non-urgent triage category (OR: 2.941, 95%CI: 2.405-3.596) ii) non-Italian-nationality (OR: 1.695, 95%CI: 1.493-1.924) and requiring psychiatric consult (OR:6.16 95%IC 4.82-7.87); while protective factors resulted: i) female gender (OR: 0.713, 95%CI: 0.633-0.803); i) Paediatric ED (OR: 0.593, 95%CI: 0.437-0.805); ii) Obstetrics-Gynaecology ED (OR: 0.284, 95%CI: 0.193-0.416) iii) inclusion in fast track pathways (OR: 0.747, 95%CI: 0.602-0.927). Higher ED leaving rate were observed during night-time and Sunday, either overcrowding resulted not associated.Conclusion: Results show the necessity to implement primary care-ED integrated pathway, mainly in frail sub-population, improve awareness on healthcare service use and refine communication skills in ED-team. (www.actabiomedica.it)
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Affiliation(s)
- Alberto Carli
- School of Specialization in Hygiene and Preventive Medicine - University of Verona.
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Alcala-Torano R, Walther M, Sommer DJ, Park CK, Ghirlanda G. Rational design of a hexameric protein assembly stabilized by metal chelation. Biopolymers 2018; 109:e23233. [PMID: 30191549 DOI: 10.1002/bip.23233] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 06/15/2018] [Accepted: 07/05/2018] [Indexed: 12/27/2022]
Abstract
Protein-based self-assembled nanostructures hold tremendous promise as smart materials. One strategy to control the assembly of individual protein modules takes advantage of the directionality and high affinity bonding afforded by metal chelation. Here, we describe the use of 2,2'-bipyridine units (Bpy) as side chains to template the assembly of large structures (MW approx. 35 000 Da) in a metal-dependent manner. The structures are trimers of independently folded 3-helix bundles, and are held together by 2 Me(Bpy)3 complexes. The assemblies are stable to thermal denaturation, and are more than 90% helical at 90°C. Circular dichroism spectroscopy shows that one of the 2 possible (Bpy)3 enantiomers is favored over the other. Because of the sequence pliability of the starting peptides, these constructs could find use to organize functional groups at controlled positions within a supramolecular assembly.
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Affiliation(s)
| | - Mathieu Walther
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
| | - Dayn J Sommer
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
| | - Chad K Park
- Department of Biochemistry, University of Arizona, Tucson, Arizona
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18
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Korendovych IV, Ghirlanda G. Editorial overview: The many facets of protein design: from self-assembled materials to vaccines. Curr Opin Struct Biol 2018; 51:iv-vi. [DOI: 10.1016/j.sbi.2018.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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19
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Sharma P, Kazan IC, Ozkan SB, Ghirlanda G. Design of Novel Lectins by Computer‐Guided Directed Evolution. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.673.24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Prerna Sharma
- School of Molecular SciencesDepartment of PhysicsArizona State UniversityTempeAZ
| | - I. Can Kazan
- School for Biological PhysicsDepartment of PhysicsArizona State UniversityTempeAZ
| | - Sefika Banu Ozkan
- School for Biological PhysicsDepartment of PhysicsArizona State UniversityTempeAZ
| | - Giovanna Ghirlanda
- School of Molecular SciencesDepartment of PhysicsArizona State UniversityTempeAZ
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20
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Affiliation(s)
- O S Salafia
- Univ. di Milano Bicocca, Dip. di Fisica ‘G. Occhialini’, Piazza della Scienza 3, I-20126 Milano, Italy
- INAF – Osservatorio Astronomico di Brera, via E. Bianchi 46, I-23807 Merate, Italy
- INFN – Sezione di Milano-Bicocca, Piazza della Scienza 3, I-20126 Milano, Italy
| | - G Ghisellini
- INAF – Osservatorio Astronomico di Brera, via E. Bianchi 46, I-23807 Merate, Italy
| | - G Ghirlanda
- INAF – Osservatorio Astronomico di Brera, via E. Bianchi 46, I-23807 Merate, Italy
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21
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Olson TL, Espiritu E, Edwardraja S, Canarie E, Flores M, Williams JC, Ghirlanda G, Allen JP. Biochemical and spectroscopic characterization of dinuclear Mn-sites in artificial four-helix bundle proteins. Biochim Biophys Acta Bioenerg 2017; 1858:945-954. [PMID: 28882760 DOI: 10.1016/j.bbabio.2017.08.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 08/28/2017] [Accepted: 08/31/2017] [Indexed: 01/18/2023]
Abstract
To better understand metalloproteins with Mn-clusters, we have designed artificial four-helix bundles to have one, two, or three dinuclear metal centers able to bind Mn(II). Circular dichroism measurements showed that the Mn-proteins have substantial α-helix content, and analysis of electron paramagnetic resonance spectra is consistent with the designed number of bound Mn-clusters. The Mn-proteins were shown to catalyze the conversion of hydrogen peroxide into molecular oxygen. The loss of hydrogen peroxide was dependent upon the concentration of protein with bound Mn, with the proteins containing multiple Mn-clusters showing greater activity. Using an oxygen sensor, the oxygen concentration was found to increase with a rate up to 0.4μM/min, which was dependent upon the concentrations of hydrogen peroxide and the Mn-protein. In addition, the Mn-proteins were shown to serve as electron donors to bacterial reaction centers using optical spectroscopy. Similar binding of the Mn-proteins to reaction centers was observed with an average dissociation constant of 2.3μM. The Mn-proteins with three metal centers were more effective at this electron transfer reaction than the Mn-proteins with one or two metal centers. Thus, multiple Mn-clusters can be incorporated into four-helix bundles with the capability of performing catalysis and electron transfer to a natural protein.
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Affiliation(s)
- Tien L Olson
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Eduardo Espiritu
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | | | - Elizabeth Canarie
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Marco Flores
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - JoAnn C Williams
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Giovanna Ghirlanda
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - James P Allen
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
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22
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Zaccardi F, Rocca B, Rizzi A, Ciminello A, Teofili L, Ghirlanda G, De Stefano V, Pitocco D. Platelet indices and glucose control in type 1 and type 2 diabetes mellitus: A case-control study. Nutr Metab Cardiovasc Dis 2017; 27:902-909. [PMID: 28838851 DOI: 10.1016/j.numecd.2017.06.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 05/23/2017] [Accepted: 06/27/2017] [Indexed: 01/13/2023]
Abstract
BACKGROUND AND AIMS The relationship between platelet indices and glucose control may differ in type 1 (T1DM) and type 2 (T2DM) diabetes. We aimed to investigate differences in mean platelet volume (MPV), platelet count, and platelet mass between patients with T1DM, T2DM, and healthy controls and to explore associations between these platelet indices and glucose control. METHODS AND RESULTS A total of 691 T1DM and 459 T2DM patients and 943 control subjects (blood donors) were included. HbA1c was measured in all subjects with diabetes and 36 T1DM patients further underwent 24 h-continuous glucose monitoring to estimate short-term glucose control (glucose mean and standard deviation). Adjusting for age and sex, platelet count was higher and MPV lower in both T1DM and T2DM patients vs control subjects, while platelet mass (MPV × platelet count) resulted higher only in T2DM. Upon further adjustment for HbA1c, differences in platelet count and mass were respectively 19.5 × 109/L (95%CI: 9.8-29.3; p < 0.001) and 101 fL/nL (12-191; p = 0.027) comparing T2DM vs T1DM patients. MPV and platelet count were significantly and differently related in T2DM patients vs both T1DM and control subjects; this difference was maintained also accounting for HbA1c, age, and sex. Platelet mass and the volume-count relationship were significantly related to HbA1c only in T1DM patients. No associations were found between platelet indices and short-term glucose control. CONCLUSION By accounting for confounders and glucose control, our data evidenced higher platelet mass and different volume-count kinetics in subjects with T2DM vs T1DM. Long-term glucose control seemed to influence platelet mass and the volume-count relationship only in T1DM subjects. These findings suggest different mechanisms behind platelet formation in T1DM and T2DM patients with long-term glycaemic control being more relevant in T1DM than T2DM.
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Affiliation(s)
- F Zaccardi
- Diabetes Research Centre, University of Leicester, Leicester, UK; Diabetes Care Unit, Catholic University School of Medicine, Rome, Italy.
| | - B Rocca
- Institute of Pharmacology, Catholic University School of Medicine, Rome, Italy
| | - A Rizzi
- Diabetes Care Unit, Catholic University School of Medicine, Rome, Italy
| | - A Ciminello
- Institute of Haematology, Catholic University School of Medicine, Rome, Italy
| | - L Teofili
- Institute of Haematology, Catholic University School of Medicine, Rome, Italy
| | - G Ghirlanda
- Diabetes Care Unit, Catholic University School of Medicine, Rome, Italy
| | - V De Stefano
- Institute of Haematology, Catholic University School of Medicine, Rome, Italy
| | - D Pitocco
- Diabetes Care Unit, Catholic University School of Medicine, Rome, Italy
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23
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Campitelli P, Zhou HX, Ghirlanda G, Ozkan SB. Dynamic Flexibility Index Sheds Light on Pin1 Allostery. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.1720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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24
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25
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Sommer DJ, Roy A, Astashkin A, Ghirlanda G. Modulation of cluster incorporation specificity in a de novo iron-sulfur cluster binding peptide. Biopolymers 2016; 104:412-8. [PMID: 25808361 DOI: 10.1002/bip.22635] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 02/10/2015] [Accepted: 02/11/2015] [Indexed: 12/20/2022]
Abstract
iron-sulfur cluster binding proteins perform an astounding variety of functions, and represent one of the most abundant classes of metalloproteins. Most often, they constitute pairs or chains and act as electron transfer modules either within complex redox enzymes or within small diffusible proteins. We have previously described the design of a three-helix bundle that can bind two clusters within its hydrophobic core. Here, we use single-point mutations to exchange one of the Cys ligands coordinating the cluster to either Leu or Ser. We show that the mutants modulate the redox potential of the clusters and stabilize the [3Fe-4S] form over the [4Fe-4S] form, supporting the use of model iron-sulfur cluster proteins as modules in the design of complex redox enzymes.
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Affiliation(s)
| | - Anindya Roy
- Chemistry and Biochemistry, Arizona State University, Tempe, AZ
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26
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Alcala-Torano R, Sommer DJ, Bahrami Dizicheh Z, Ghirlanda G. Design Strategies for Redox Active Metalloenzymes: Applications in Hydrogen Production. Methods Enzymol 2016; 580:389-416. [PMID: 27586342 DOI: 10.1016/bs.mie.2016.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
The last decades have seen an increased interest in finding alternative means to produce renewable fuels in order to satisfy the growing energy demands and to minimize environmental impact. Nature can serve as an inspiration for development of these methodologies, as enzymes are able to carry out a wide variety of redox processes at high efficiency, employing a wide array of earth-abundant transition metals to do so. While it is well recognized that the protein environment plays an important role in tuning the properties of the different metal centers, the structure/function relationships between amino acids and catalytic centers are not well resolved. One specific approach to study the role of proteins in both electron and proton transfer is the biomimetic design of redox active peptides, binding organometallic clusters in well-understood protein environments. Here we discuss different strategies for the design of peptides incorporating redox active FeS clusters, [FeFe]-hydrogenase organometallic mimics, and porphyrin centers into different peptide and protein environments in order to understand natural redox enzymes.
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Affiliation(s)
- R Alcala-Torano
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States
| | - D J Sommer
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States
| | - Z Bahrami Dizicheh
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States
| | - G Ghirlanda
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States.
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27
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Woodrum BW, Maxwell J, Allen DM, Wilson J, Krumpe LRH, Bobkov AA, Hill RB, Kibler KV, O'Keefe BR, Ghirlanda G. A Designed "Nested" Dimer of Cyanovirin-N Increases Antiviral Activity. Viruses 2016; 8:v8060158. [PMID: 27275831 PMCID: PMC4926178 DOI: 10.3390/v8060158] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 05/26/2016] [Accepted: 05/30/2016] [Indexed: 12/19/2022] Open
Abstract
Cyanovirin-N (CV-N) is an antiviral lectin with potent activity against enveloped viruses, including HIV. The mechanism of action involves high affinity binding to mannose-rich glycans that decorate the surface of enveloped viruses. In the case of HIV, antiviral activity of CV-N is postulated to require multivalent interactions with envelope protein gp120, achieved through a pseudo-repeat of sequence that adopts two near-identical glycan-binding sites, and possibly involves a 3D-domain-swapped dimeric form of CV-N. Here, we present a covalent dimer of CV-N that increases the number of active glycan-binding sites, and we characterize its ability to recognize four glycans in solution. A CV-N variant was designed in which two native repeats were separated by the “nested” covalent insertion of two additional repeats of CV-N, resulting in four possible glycan-binding sites. The resulting Nested CV-N folds into a wild-type-like structure as assessed by circular dichroism and NMR spectroscopy, and displays high thermal stability with a Tm of 59 °C, identical to WT. All four glycan-binding domains encompassed by the sequence are functional as demonstrated by isothermal titration calorimetry, which revealed two sets of binding events to dimannose with dissociation constants Kd of 25 μM and 900 μM, assigned to domains B and B’ and domains A and A’ respectively. Nested CV-N displays a slight increase in activity when compared to WT CV-N in both an anti-HIV cellular assay and a fusion assay. This construct conserves the original binding specifityies of domain A and B, thus indicating correct fold of the two CV-N repeats. Thus, rational design can be used to increase multivalency in antiviral lectins in a controlled manner.
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Affiliation(s)
- Brian W Woodrum
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
| | - Jason Maxwell
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
| | - Denysia M Allen
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
| | - Jennifer Wilson
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA.
| | - Lauren R H Krumpe
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, MD 21702, USA.
| | - Andrey A Bobkov
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.
| | - R Blake Hill
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
| | - Karen V Kibler
- School of Life Sciences and The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.
| | - Barry R O'Keefe
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA.
| | - Giovanna Ghirlanda
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
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28
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Li Z, Bolia A, Maxwell JD, Bobkov AA, Ghirlanda G, Ozkan SB, Margulis CJ. A Rigid Hinge Region Is Necessary for High-Affinity Binding of Dimannose to Cyanovirin and Associated Constructs. Biochemistry 2015; 54:6951-60. [PMID: 26507789 DOI: 10.1021/acs.biochem.5b00635] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Mutations in the hinge region of cyanovirin-N (CVN) dictate its preferential oligomerization state. Constructs with the Pro51Gly mutation preferentially exist as monomers, whereas wild-type cyanovirin can form domain-swapped dimers under certain conditions. Because the hinge region is an integral part of the high-affinity binding site of CVN, we investigated whether this mutation affects the shape, flexibility, and binding affinity of domain B for dimannose. Our studies indicate that the capability of monomeric wild-type CVN to resist mechanical perturbations is enhanced when compared to that of constructs in which the hinge region is more flexible. Our computational results also show that enhanced flexibility leads to blocking of the binding site by allowing different rotational isomeric states of Asn53. Moreover, at higher temperatures, this observed flexibility leads to an interaction between Asn53 and Asn42, further hindering access to the binding site. On the basis of these results, we predicted that binding affinity for dimannose would be more favorable for cyanovirin constructs containing a wild-type hinge region, whereas affinity would be impaired in the case of mutants containing Pro51Gly. Experimental characterization by isothermal titration calorimetry of a set of cyanovirin mutants confirms this hypothesis. Those possessing the Pro51Gly mutation are consistently inferior binders.
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Affiliation(s)
- Zhen Li
- Department of Chemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Ashini Bolia
- Department of Chemistry and Biochemistry, Arizona State University , Tempe, Arizona 85287-1604, United States
| | - Jason D Maxwell
- Department of Chemistry and Biochemistry, Arizona State University , Tempe, Arizona 85287-1604, United States
| | - Andrey A Bobkov
- Sanford Burnham Medical Research Institute , 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Giovanna Ghirlanda
- Department of Chemistry and Biochemistry, Arizona State University , Tempe, Arizona 85287-1604, United States
| | - S Banu Ozkan
- Center for Biological Physics, Department of Physics, Arizona State University , Tempe, Arizona 85287, United States
| | - Claudio J Margulis
- Department of Chemistry, University of Iowa , Iowa City, Iowa 52242, United States
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29
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Flory JD, Johnson T, Simmons CR, Lin S, Ghirlanda G, Fromme P. Purification and assembly of thermostable Cy5 labeled γ-PNAs into a 3D DNA nanocage. Artif DNA PNA XNA 2015; 5:1-8. [PMID: 25760314 DOI: 10.4161/1949095x.2014.992181] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
PNA is hybrid molecule ideally suited for bridging the functional landscape of polypeptides with the structural diversity that can be engineered with DNA nanostructures. However, PNA can be more challenging to work with in aqueous solvents due to its hydrophobic nature. A solution phase method using strain promoted, copper free click chemistry was developed to conjugate the fluorescent dye Cy5 to 2 bifunctional PNA strands as a first step toward building cyclic PNA-polypeptides that can be arranged within 3D DNA nanoscaffolds. A 3D DNA nanocage was designed with binding sites for the 2 fluorescently labeled PNA strands in close proximity to mimic protein active sites. Denaturing polyacrylamide gel electrophoresis (PAGE) is introduced as an efficient method for purifying charged, dye-labeled PNA conjugates from large excesses of unreacted dye and unreacted, neutral PNA. Elution from the gel in water was monitored by fluorescence and found to be more efficient for the more soluble PNA strand. Native PAGE shows that both PNA strands hybridize to their intended binding sites within the DNA nanocage. Förster resonance energy transfer (FRET) with a Cy3 labeled DNA nanocage was used to determine the dissociation temperature of one PNA-Cy5 conjugate to be near 50°C. Steady-state and time resolved fluorescence was used to investigate the dye orientation and interactions within the various complexes. Bifunctional, thermostable PNA molecules are intriguing candidates for controlling the assembly and orientation of peptides within small DNA nanocages for mimicking protein catalytic sites.
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Key Words
- DBCO, dibenzocyclooctyl
- DNA nanotechnology
- DTNB, 5, 5′-dithiobis-(2-nitrobenzoic acid)
- EtBr, ethidium bromide
- IEX-FPLC, ion-exchange fast protein liquid chromatography
- MALDI-MS, matrix assisted laser desorption ionization mass spectrometry
- PAGE, polyacrylamide gel electrophoresis
- PNA, peptide nucleic acid
- RP-HPLC, reverse-phase high pressure liquid chromatography
- TCEP, tris(2-carboxyethyl)phosphine
- biomimicry
- copper-free click chemistry
- fluorescence
- self-assembly
- γ-PNA
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Affiliation(s)
- Justin D Flory
- a Department of Chemistry and Biochemistry; Arizona State University ; Tempe , Arizona USA
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30
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Olson TL, Espiritu E, Edwardraja S, Simmons CR, Williams JC, Ghirlanda G, Allen JP. Design of dinuclear manganese cofactors for bacterial reaction centers. Biochim Biophys Acta 2015; 1857:539-547. [PMID: 26392146 DOI: 10.1016/j.bbabio.2015.09.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 09/14/2015] [Indexed: 12/28/2022]
Abstract
A compelling target for the design of electron transfer proteins with novel cofactors is to create a model for the oxygen-evolving complex, a Mn4Ca cluster, of photosystem II. A mononuclear Mn cofactor can be added to the bacterial reaction center, but the addition of multiple metal centers is constrained by the native protein architecture. Alternatively, metal centers can be incorporated into artificial proteins. Designs for the addition of dinuclear metal centers to four-helix bundles resulted in three artificial proteins with ligands for one, two, or three dinuclear metal centers able to bind Mn. The three-dimensional structure determined by X-ray crystallography of one of the Mn-proteins confirmed the design features and revealed details concerning coordination of the Mn center. Electron transfer between these artificial Mn-proteins and bacterial reaction centers was investigated using optical spectroscopy. After formation of a light-induced, charge-separated state, the experiments showed that the Mn-proteins can donate an electron to the oxidized bacteriochlorophyll dimer of modified reaction centers, with the Mn-proteins having additional metal centers being more effective at this electron transfer reaction. Modeling of the structure of the Mn-protein docked to the reaction center showed that the artificial protein likely binds on the periplasmic surface similarly to cytochrome c2, the natural secondary donor. Combining reaction centers with exogenous artificial proteins provides the opportunity to create ligands and investigate the influence of inhomogeneous protein environments on multinuclear redox-active metal centers. This article is part of a Special Issue entitled Biodesign for Bioenergetics--the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.
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Affiliation(s)
- Tien L Olson
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Eduardo Espiritu
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | | | - Chad R Simmons
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - JoAnn C Williams
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Giovanna Ghirlanda
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - James P Allen
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
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31
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Flores M, Olson TL, Wang D, Edwardraja S, Shinde S, Williams JC, Ghirlanda G, Allen JP. Copper Environment in Artificial Metalloproteins Probed by Electron Paramagnetic Resonance Spectroscopy. J Phys Chem B 2015. [DOI: 10.1021/acs.jpcb.5b04172] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Marco Flores
- Department
of Chemistry and
Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Tien L. Olson
- Department
of Chemistry and
Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Dong Wang
- Department
of Chemistry and
Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Selvakumar Edwardraja
- Department
of Chemistry and
Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Sandip Shinde
- Department
of Chemistry and
Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - JoAnn C. Williams
- Department
of Chemistry and
Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Giovanna Ghirlanda
- Department
of Chemistry and
Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - James P. Allen
- Department
of Chemistry and
Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
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32
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Pietravalle P, Morano S, De Rossi MG, Mariani G, Cristina G, Ghirlanda G, Cotroneo P, Clementi A, Di Mario U. Protein charge permselectivity in type 2 and type 1 diabetes. Contrib Nephrol 2015; 101:135-8. [PMID: 8467666 DOI: 10.1159/000422121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- P Pietravalle
- Department of Endocrinology Clinica Medica 2, University La Sapienza, Rome, Italy
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33
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Flory JD, Johnson T, Simmons CR, Lin S, Ghirlanda G, Fromme P. Purification and assembly of thermostable Cy5 labeled γ-PNAs into a 3D DNA nanocage. Artif DNA PNA XNA 2014; 5:e992181. [PMID: 27430048 PMCID: PMC5329897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 06/27/2014] [Accepted: 11/24/2014] [Indexed: 03/25/2024]
Abstract
PNA is hybrid molecule ideally suited for bridging the functional landscape of polypeptides with the structural diversity that can be engineered with DNA nanostructures. However, PNA can be more challenging to work with in aqueous solvents due to its hydrophobic nature. A solution phase method using strain promoted, copper free click chemistry was developed to conjugate the fluorescent dye Cy5 to 2 bifunctional PNA strands as a first step toward building cyclic PNA-polypeptides that can be arranged within 3D DNA nanoscaffolds. A 3D DNA nanocage was designed with binding sites for the 2 fluorescently labeled PNA strands in close proximity to mimic protein active sites. Denaturing polyacrylamide gel electrophoresis (PAGE) is introduced as an efficient method for purifying charged, dye-labeled NA conjugates from large excesses of unreacted dye and unreacted, neutral PNA. Elution from the gel in water was monitored by fluorescence and found to be more efficient for the more soluble PNA strand. Native PAGE shows that both PNA strands hybridize to their intended binding sites within the DNA nanocage. Förster resonance energy transfer (FRET) with a Cy3 labeled DNA nanocage was used to determine the dissociation temperature of one PNA-Cy5 conjugate to be near 50C. Steady-state and time resolved fluorescence was used to investigate the dye orientation and interactions within the various complexes. Bifunctional, thermostable PNA molecules are intriguing candidates for controlling the assembly and orientation of peptides within small DNA nanocages for mimicking protein catalytic sites.
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Affiliation(s)
- Justin D Flory
- Department of Chemistry and Biochemistry; Arizona State University; Tempe, Arizona USA
- Center for Bio-Inspired Solar Fuel Production; Arizona State University; Tempe, AZ USA
| | - Trey Johnson
- Department of Chemistry and Biochemistry; Arizona State University; Tempe, Arizona USA
- Center for Bio-Inspired Solar Fuel Production; Arizona State University; Tempe, AZ USA
| | - Chad R Simmons
- Department of Chemistry and Biochemistry; Arizona State University; Tempe, Arizona USA
- Center for Bio-Inspired Solar Fuel Production; Arizona State University; Tempe, AZ USA
- Biodesign Institute; Arizona State University; Tempe, Arizona USA
| | - Su Lin
- Department of Chemistry and Biochemistry; Arizona State University; Tempe, Arizona USA
- Biodesign Institute; Arizona State University; Tempe, Arizona USA
| | - Giovanna Ghirlanda
- Department of Chemistry and Biochemistry; Arizona State University; Tempe, Arizona USA
- Center for Bio-Inspired Solar Fuel Production; Arizona State University; Tempe, AZ USA
| | - Petra Fromme
- Department of Chemistry and Biochemistry; Arizona State University; Tempe, Arizona USA
- Center for Bio-Inspired Solar Fuel Production; Arizona State University; Tempe, AZ USA
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34
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Roy A, Sommer DJ, Schmitz RA, Brown CL, Gust D, Astashkin A, Ghirlanda G. A De Novo Designed 2[4Fe-4S] Ferredoxin Mimic Mediates Electron Transfer. J Am Chem Soc 2014; 136:17343-9. [DOI: 10.1021/ja510621e] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Anindya Roy
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Dayn Joseph Sommer
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Robert Arthur Schmitz
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Chelsea Lynn Brown
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Devens Gust
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Andrei Astashkin
- Department
of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Giovanna Ghirlanda
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
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35
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Bolia A, Woodrum BW, Cereda A, Ruben MA, Wang X, Ozkan SB, Ghirlanda G. A flexible docking scheme efficiently captures the energetics of glycan-cyanovirin binding. Biophys J 2014; 106:1142-51. [PMID: 24606938 DOI: 10.1016/j.bpj.2014.01.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 01/08/2014] [Accepted: 01/10/2014] [Indexed: 01/10/2023] Open
Abstract
Cyanovirin-N (CVN), a cyanobacterial lectin, exemplifies a class of antiviral agents that inhibit HIV by binding to the highly glycosylated envelope protein gp120. Here, we investigate the energetics of glycan recognition using a computationally inexpensive flexible docking approach, backbone perturbation docking (BP-Dock). We benchmarked our method using two mutants of CVN: P51G-m4-CVN, which binds dimannose with high affinity through domain B, and CVN((mutDB)), in which binding to domain B has been abolished through mutation of five polar residues to small nonpolar side chains. We investigated the energetic contribution of these polar residues along with the additional position 53 by docking dimannose to single-point CVN mutant models. Analysis of the docking simulations indicated that the E41A/G and T57A mutations led to a significant decrease in binding energy scores due to rearrangements of the hydrogen-bond network that reverberated throughout the binding cavity. N42A decreased the binding score to a level comparable to that of CVN((mutDB)) by affecting the integrity of the local protein structure. In contrast, N53S resulted in a high binding energy score, similar to P51G-m4-CVN. Experimental characterization of the five mutants by NMR spectroscopy confirmed the binding affinity pattern predicted by BP-Dock. Despite their mostly conserved fold and stability, E41A, E41G, and T57A displayed dissociation constants in the millimolar range. N53S showed a binding constant in the low micromolar range, similar to that observed for P51G-m4-CVN. No binding was observed for N42A. Our results show that BP-Dock is a useful tool for rapidly screening the relative binding affinity pattern of in silico-designed mutants compared with wild-type, supporting its use to design novel mutants with enhanced binding properties.
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Affiliation(s)
- Ashini Bolia
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona
| | - Brian W Woodrum
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona
| | - Angelo Cereda
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona
| | - Melissa A Ruben
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona
| | - Xu Wang
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona
| | - S Banu Ozkan
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, Arizona.
| | - Giovanna Ghirlanda
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, Arizona.
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36
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Shinde S, Binder JK, Goyal B, Woodrum B, De Munari S, Levitus M, Ghirlanda G. A designed buried salt bridge modulates heterodimerization of a membrane peptide. Biopolymers 2014; 102:437-43. [PMID: 25250823 DOI: 10.1002/bip.22564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 08/19/2014] [Accepted: 09/05/2014] [Indexed: 11/07/2022]
Abstract
Specific helix-helix interactions underpin the correct assembly of multipass membrane proteins. Here, we show that a designed buried salt bridge mediates heterodimer formation of model transmembrane helical peptides in a pH-dependent manner. The model peptides bear side chains functionalized with either a carboxylic acid or a primary amine within a hydrophobic segment. The association behavior was monitored by Förster resonance energy transfer, revealing that heterodimer formation is maximized at a pH close to neutrality (pH 6.5), at which each peptide is found in a charged state. In contrast, heterodimerization is disfavored at low and high values of pH, because either the carboxylic acid or the primary amine is present in its neutral state, thus preventing the formation of a salt bridge. These findings provide a blueprint for the design and modulation of protein-protein interactions in membrane proteins.
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Affiliation(s)
- Sandip Shinde
- Chemistry and Biochemistry, Arizona State University, Tempe, AZ
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37
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Pitocco D, Marano R, Di Stasio E, Scavone G, Savino G, Zaccardi F, Rizzi A, Martini F, Musella T, Silvestri V, Costantini F, Galli M, Caputo S, Bonomo L, Ghirlanda G. Atherosclerotic coronary plaque in subjects with diabetic neuropathy: the prognostic cardiovascular role of Charcot neuroarthropathy--a case-control study. Acta Diabetol 2014; 51:587-93. [PMID: 24509841 DOI: 10.1007/s00592-014-0559-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 01/15/2014] [Indexed: 11/24/2022]
Abstract
The aim of this study was to investigate the severity of coronary artery disease (CAD) and the plaque composition in neuropathic type 2 diabetic subjects with and without Charcot neuroarthropathy (CN) undergoing multidetector computed tomography coronary angiography (MDCT-CA). The study was a single-center, observational, with unmatched case-control design. We selected 17 CN patients and 18 patients with diabetic neuropathy (DN) without CN. In all the patients, multidetector computed tomography was performed to assess the coronary artery calcium score (CACS) and degree of coronary artery stenosis. Patients were classified as positive in the presence of significant CAD if there was at least one stenosis >50 % on MDCT-CA. The invasive coronary angiography was performed in case of significant stenosis detected with MDCT-CA, both as reference to standard and eventually as treatment. Groups were matched for age, sex, and traditional CAD risk factors. As compared to DN individuals, CN exhibited higher rates of significant coronary stenoses (p = 0.027; OR 7.7 [1.3-43.5]). However, no significant differences were observed in the CACS, which reflects plaque burden, in the two groups (p = 0.759). No significant differences were observed comparing CACS distribution in all subjects for stenosis higher/equal or lower than 50 % (p = 0.320). Finally, no significant differences were observed comparing CACS distribution in CN and DN subjects for coronary stenoses higher/equal or lower than 50 %. Our results suggest that CN patients have a higher prevalence of severe coronary plaques compared to DN patients. Nevertheless, coronary plaques in CN patients did not exhibit an increased degree of calcification.
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Affiliation(s)
- D Pitocco
- Department of Internal Medicine, Catholic University School of Medicine, Rome, Italy,
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38
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Affiliation(s)
- Dong Wang
- Department of Chemistry and
Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Giovanna Ghirlanda
- Department of Chemistry and
Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - James P. Allen
- Department of Chemistry and
Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
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39
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Flory JD, Simmons CR, Lin S, Johnson T, Andreoni A, Zook J, Ghirlanda G, Liu Y, Yan H, Fromme P. Low temperature assembly of functional 3D DNA-PNA-protein complexes. J Am Chem Soc 2014; 136:8283-95. [PMID: 24871902 DOI: 10.1021/ja501228c] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Proteins have evolved to carry out nearly all the work required of living organisms within complex inter- and intracellular environments. However, systematically investigating the range of interactions experienced by a protein that influence its function remains challenging. DNA nanostructures are emerging as a convenient method to arrange a broad range of guest molecules. However, flexible methods are needed for arranging proteins in more biologically relevant 3D geometries under mild conditions that preserve protein function. Here we demonstrate how peptide nucleic acid (PNA) can be used to control the assembly of cytochrome c (12.5 kDa, pI 10.5) and azurin (13.9 kDa, pI 5.7) proteins into separate 3D DNA nanocages, in a process that maintains protein function. Toehold-mediated DNA strand displacement is introduced as a method to purify PNA-protein conjugates. The PNA-proteins were assembled within 2 min at room temperature and within 4 min at 11 °C, and hybridize with even greater efficiency than PNA conjugated to a short peptide. Gel electrophoresis and steady state and time-resolved fluorescence spectroscopy were used to investigate the effect of protein surface charge on its interaction with the negatively charged DNA nanocage. These data were used to generate a model of the DNA-PNA-protein complexes that show the negatively charged azurin protein repelled away from the DNA nanocage while the positively charged cytochrome c protein remains within and closely interacts with the DNA nanocage. When conjugated to PNA and incorporated into the DNA nanocage, the cytochrome c secondary structure and catalytic activity were maintained, and its redox potential was reduced modestly by 20 mV possibly due to neutralization of some positive surface charges. This work demonstrates a flexible new approach for using 3D nucleic acid (PNA-DNA) nanostructures to control the assembly of functional proteins, and facilitates further investigation of protein interactions as well as engineer more elaborate 3D protein complexes.
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Affiliation(s)
- Justin D Flory
- Department of Chemistry and Biochemistry, ‡Center for Bio-Inspired Solar Fuel Production, and §Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
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40
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Cope SM, Shinde S, Best RB, Ghirlanda G, Vaiana SM. Cyclic N-terminal loop of amylin forms non amyloid fibers. Biophys J 2014; 105:1661-9. [PMID: 24094407 DOI: 10.1016/j.bpj.2013.08.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 08/17/2013] [Accepted: 08/21/2013] [Indexed: 10/26/2022] Open
Abstract
We report for the first time, to our knowledge, that the N-terminal loop (N_loop) of amylin (islet amyloid polypeptide (IAPP) residues 1-8) forms extremely long and stable non-β-sheet fibers in solution under the same conditions in which human amylin (hIAPP) forms amyloid fibers. This observation applies to the cyclic, oxidized form of the N_loop but not to the linear, reduced form, which does not form fibers. Our findings indicate a potential role of direct N_loop-N_loop interactions in hIAPP aggregation, which has not been previously explored, with important implications for the mechanism of hIAPP amyloid fiber formation, the inhibitory action of IAPP variants, and the competition between ordered and disordered aggregation in peptides of the calcitonin peptide family.
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Affiliation(s)
- Stephanie M Cope
- Center for Biological Physics, Arizona State University, Tempe, Arizona; Department of Physics, Arizona State University, Tempe, Arizona
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41
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Maselli A, Melandri A, Nava L, Mundell CG, Kawai N, Campana S, Covino S, Cummings JR, Cusumano G, Evans PA, Ghirlanda G, Ghisellini G, Guidorzi C, Kobayashi S, Kuin P, La Parola V, Mangano V, Oates S, Sakamoto T, Serino M, Virgili F, Zhang BB, Barthelmy S, Beardmore A, Bernardini MG, Bersier D, Burrows D, Calderone G, Capalbi M, Chiang J, D’Avanzo P, D’Elia V, De Pasquale M, Fugazza D, Gehrels N, Gomboc A, Harrison R, Hanayama H, Japelj J, Kennea J, Kopac D, Kouveliotou C, Kuroda D, Levan A, Malesani D, Marshall F, Nousek J, O’Brien P, Osborne JP, Pagani C, Page KL, Page M, Perri M, Pritchard T, Romano P, Saito Y, Sbarufatti B, Salvaterra R, Steele I, Tanvir N, Vianello G, Wiegand B, Wiersema K, Yatsu Y, Yoshii T, Tagliaferri G. GRB 130427A: A Nearby Ordinary Monster. Science 2014; 343:48-51. [DOI: 10.1126/science.1242279] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- A. Maselli
- Istituto Nazionale di Astrofisica (INAF)–Istituto di Astrofisica Spaziale e Fisica Cosmica (IASF) Palermo, Via Ugo La Malfa 153 I-90146 Palermo, Italy
| | - A. Melandri
- INAF–Osservatorio Astronomico di Brera, via E. Bianchi 46, I-23807 Merate, Italy
| | - L. Nava
- INAF–Osservatorio Astronomico di Brera, via E. Bianchi 46, I-23807 Merate, Italy
- AstroParticule et Cosmologie, Université Paris Diderot, CNRS/IN2P3, Commissariat à l'Energie Atomique et aux Energies Alternatives/Institut de Recherches sur les lois Fondamentales de l’Univers, Observatoire de Paris, Sorbonne Paris Cité, France
| | - C. G. Mundell
- Astrophysics Research Institute, Liverpool John Moores University, Liverpool Science Park, 146 Brownlow Hill, Liverpool L3 5RF, UK
| | - N. Kawai
- Department of Physics, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
- Coordinated Space Observation and Experiment Research Group, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - S. Campana
- INAF–Osservatorio Astronomico di Brera, via E. Bianchi 46, I-23807 Merate, Italy
| | - S. Covino
- INAF–Osservatorio Astronomico di Brera, via E. Bianchi 46, I-23807 Merate, Italy
| | - J. R. Cummings
- University of Maryland, Baltimore County/Center for Research and Exploration in Space Science & Technology/NASA Goddard Space Flight Center, Code 661, Greenbelt, MD 20771, USA
| | - G. Cusumano
- Istituto Nazionale di Astrofisica (INAF)–Istituto di Astrofisica Spaziale e Fisica Cosmica (IASF) Palermo, Via Ugo La Malfa 153 I-90146 Palermo, Italy
| | - P. A. Evans
- Department of Physics and Astronomy, University of Leicester, Leicester, LE1 7RH, UK
| | - G. Ghirlanda
- INAF–Osservatorio Astronomico di Brera, via E. Bianchi 46, I-23807 Merate, Italy
| | - G. Ghisellini
- INAF–Osservatorio Astronomico di Brera, via E. Bianchi 46, I-23807 Merate, Italy
| | - C. Guidorzi
- Department of Physics, University of Ferrara, via Saragat 1, I-44122, Ferrara, Italy
| | - S. Kobayashi
- Astrophysics Research Institute, Liverpool John Moores University, Liverpool Science Park, 146 Brownlow Hill, Liverpool L3 5RF, UK
| | - P. Kuin
- Mullard Space Science Laboratory, University College London, Holmbury St. Mary, Dorking, Surrey RH5 6NT, UK
| | - V. La Parola
- Istituto Nazionale di Astrofisica (INAF)–Istituto di Astrofisica Spaziale e Fisica Cosmica (IASF) Palermo, Via Ugo La Malfa 153 I-90146 Palermo, Italy
| | - V. Mangano
- Istituto Nazionale di Astrofisica (INAF)–Istituto di Astrofisica Spaziale e Fisica Cosmica (IASF) Palermo, Via Ugo La Malfa 153 I-90146 Palermo, Italy
- Department of Astronomy and Astrophysics, Pennsylvania State University, 525 Davey Lab, University Park, PA 16802, USA
| | - S. Oates
- Mullard Space Science Laboratory, University College London, Holmbury St. Mary, Dorking, Surrey RH5 6NT, UK
| | - T. Sakamoto
- Department of Physics and Mathematics, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan
| | - M. Serino
- Coordinated Space Observation and Experiment Research Group, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - F. Virgili
- Astrophysics Research Institute, Liverpool John Moores University, Liverpool Science Park, 146 Brownlow Hill, Liverpool L3 5RF, UK
| | - B.-B. Zhang
- Department of Astronomy and Astrophysics, Pennsylvania State University, 525 Davey Lab, University Park, PA 16802, USA
| | - S. Barthelmy
- NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA
| | - A. Beardmore
- Department of Physics and Astronomy, University of Leicester, Leicester, LE1 7RH, UK
| | - M. G. Bernardini
- INAF–Osservatorio Astronomico di Brera, via E. Bianchi 46, I-23807 Merate, Italy
| | - D. Bersier
- Astrophysics Research Institute, Liverpool John Moores University, Liverpool Science Park, 146 Brownlow Hill, Liverpool L3 5RF, UK
| | - D. Burrows
- Department of Astronomy and Astrophysics, Pennsylvania State University, 525 Davey Lab, University Park, PA 16802, USA
| | - G. Calderone
- INAF–Osservatorio Astronomico di Brera, via E. Bianchi 46, I-23807 Merate, Italy
- Dipartimento di Fisica “G. Occhialini,” Università di Milano-Bicocca, Piazza della Scienza 3, I-20126 Milano, Italy
| | - M. Capalbi
- Istituto Nazionale di Astrofisica (INAF)–Istituto di Astrofisica Spaziale e Fisica Cosmica (IASF) Palermo, Via Ugo La Malfa 153 I-90146 Palermo, Italy
| | - J. Chiang
- W. W. Hansen Experimental Physics Laboratory, Kavli Institute for Particle Astrophysics and Cosmology, Department of Physics, and SLAC National Accelerator Laboratory, Stanford University, Stanford, CA 94305, USA
| | - P. D’Avanzo
- INAF–Osservatorio Astronomico di Brera, via E. Bianchi 46, I-23807 Merate, Italy
| | - V. D’Elia
- INAF/Rome Astronomical Observatory, via Frascati 33, 00040 Monteporzio Catone (Roma), Italy
- Agenzia Spaziale Italiana (ASI) Science Data Centre, Via Galileo Galilei, 00044 Frascati (Roma), Italy
| | - M. De Pasquale
- Mullard Space Science Laboratory, University College London, Holmbury St. Mary, Dorking, Surrey RH5 6NT, UK
| | - D. Fugazza
- INAF–Osservatorio Astronomico di Brera, via E. Bianchi 46, I-23807 Merate, Italy
| | - N. Gehrels
- NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA
| | - A. Gomboc
- Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19 1000, Ljubljana, Slovenia
- Centre of Excellence Space-si, Askerceva cesta 12, 1000 Ljubljana, Slovenia
| | - R. Harrison
- Astrophysics Research Institute, Liverpool John Moores University, Liverpool Science Park, 146 Brownlow Hill, Liverpool L3 5RF, UK
| | - H. Hanayama
- Ishigakijima Astronomical Observatory, National Astronomical Observatory of Japan, 1024-1 Arakawa, Ishigaki, Okinawa 907-0024, Japan
| | - J. Japelj
- Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19 1000, Ljubljana, Slovenia
| | - J. Kennea
- Department of Astronomy and Astrophysics, Pennsylvania State University, 525 Davey Lab, University Park, PA 16802, USA
| | - D. Kopac
- Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19 1000, Ljubljana, Slovenia
| | - C. Kouveliotou
- Space Science Office, VP62, NASA/Marshall Space Flight Center, Huntsville, AL 35812, USA
| | - D. Kuroda
- Okayama Astrophysical Observatory, National Astronomical Observatory of Japan, 3037-5 Honjo, Kamogata, Asaguchi, Okayama 719-0232
| | - A. Levan
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK
| | - D. Malesani
- Dark Cosmology Centre (DARK), Niels Bohr Institute, University of Copenhagen, Juliane Maries Vej 30, 2100 Copenhagen, Denmark
| | - F. Marshall
- NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA
| | - J. Nousek
- Department of Astronomy and Astrophysics, Pennsylvania State University, 525 Davey Lab, University Park, PA 16802, USA
| | - P. O’Brien
- Department of Physics and Astronomy, University of Leicester, Leicester, LE1 7RH, UK
| | - J. P. Osborne
- Department of Physics and Astronomy, University of Leicester, Leicester, LE1 7RH, UK
| | - C. Pagani
- Department of Physics and Astronomy, University of Leicester, Leicester, LE1 7RH, UK
| | - K. L. Page
- Department of Physics and Astronomy, University of Leicester, Leicester, LE1 7RH, UK
| | - M. Page
- Mullard Space Science Laboratory, University College London, Holmbury St. Mary, Dorking, Surrey RH5 6NT, UK
| | - M. Perri
- INAF/Rome Astronomical Observatory, via Frascati 33, 00040 Monteporzio Catone (Roma), Italy
- Agenzia Spaziale Italiana (ASI) Science Data Centre, Via Galileo Galilei, 00044 Frascati (Roma), Italy
| | - T. Pritchard
- Department of Astronomy and Astrophysics, Pennsylvania State University, 525 Davey Lab, University Park, PA 16802, USA
| | - P. Romano
- Istituto Nazionale di Astrofisica (INAF)–Istituto di Astrofisica Spaziale e Fisica Cosmica (IASF) Palermo, Via Ugo La Malfa 153 I-90146 Palermo, Italy
| | - Y. Saito
- Department of Physics, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - B. Sbarufatti
- INAF–Osservatorio Astronomico di Brera, via E. Bianchi 46, I-23807 Merate, Italy
- Department of Astronomy and Astrophysics, Pennsylvania State University, 525 Davey Lab, University Park, PA 16802, USA
| | - R. Salvaterra
- INAF-IASF Milano, via E. Bassini 15, I-20133 Milano, Italy
| | - I. Steele
- Astrophysics Research Institute, Liverpool John Moores University, Liverpool Science Park, 146 Brownlow Hill, Liverpool L3 5RF, UK
| | - N. Tanvir
- Department of Physics and Astronomy, University of Leicester, Leicester, LE1 7RH, UK
| | - G. Vianello
- W. W. Hansen Experimental Physics Laboratory, Kavli Institute for Particle Astrophysics and Cosmology, Department of Physics, and SLAC National Accelerator Laboratory, Stanford University, Stanford, CA 94305, USA
| | - B. Wiegand
- NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA
| | - K. Wiersema
- Department of Physics and Astronomy, University of Leicester, Leicester, LE1 7RH, UK
| | - Y. Yatsu
- Department of Physics, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - T. Yoshii
- Department of Physics, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - G. Tagliaferri
- INAF–Osservatorio Astronomico di Brera, via E. Bianchi 46, I-23807 Merate, Italy
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42
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Cope SM, Sizemore SM, Roy A, Ghirlanda G, Vaiana SM. Structure and Internal Dynamics of Calcitonin Family Peptides: Implications for Amyloid Formation. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.3802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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43
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Sizemore SM, Cope SM, Roy A, Ghirlanda G, Vaiana SM. Solvent Effects on the Structure and Internal Dynamics of Calcitonin Gene-Related Peptide. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.1588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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44
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Sommer DJ, Vaughn MD, Ghirlanda G. Protein secondary-shell interactions enhance the photoinduced hydrogen production of cobalt protoporphyrin IX. Chem Commun (Camb) 2014; 50:15852-5. [DOI: 10.1039/c4cc06700b] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
An efficient molecular catalyst for hydrogen production is generated by incorporating Co-protoporphyrin IX into myoglobin. The activity is modulated by engineered mutations.
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45
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Faiella M, Roy A, Sommer D, Ghirlanda G. De novo design of functional proteins: Toward artificial hydrogenases. Biopolymers 2013; 100:558-71. [DOI: 10.1002/bip.22420] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 07/08/2013] [Accepted: 09/18/2013] [Indexed: 12/18/2022]
Affiliation(s)
- Marina Faiella
- Department of Chemistry and Biochemistry; Arizona State University; Tempe AZ
| | - Anindya Roy
- Department of Chemistry and Biochemistry; Arizona State University; Tempe AZ
| | - Dayn Sommer
- Department of Chemistry and Biochemistry; Arizona State University; Tempe AZ
| | - Giovanna Ghirlanda
- Department of Chemistry and Biochemistry; Arizona State University; Tempe AZ
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46
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Affiliation(s)
- Anindya Roy
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Iosifina Sarrou
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Michael D. Vaughn
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Andrei V. Astashkin
- Department
of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Giovanna Ghirlanda
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
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47
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Pitocco D, Rizzi A, Scavone G, Tanese L, Zaccardi F, Manto A, Ghirlanda G. Fields of application of continuous subcutaneous insulin infusion in the treatment of diabetes and implications in the use of rapid-acting insulin analogues. MINERVA ENDOCRINOL 2013; 38:321-328. [PMID: 24126552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In western countries, diabetes mellitus, because of macrovascular and microvascular complications related to it, is still an important cause of death. Patients with type 1 diabetes mellitus (T1DM) have a six-time higher risk of mortality than healthy patients. Since the Diabetes Control and Complications Trial (DCCT) established how an intensive therapy is necessary to prevent diabetes mellitus complications, many studies have been conducted to understand which method is able to reach an optimal metabolic control. In the past 30 years continuous subcutaneous insulin infusion established/introduced as a validate alternative to multiple daily injections. Several trials demonstrated that, when compared to MDI, CSII brings to a better metabolic control, in terms of a reduction of glycated hemoglobin and blood glucose variability, hypoglycemic episodes and improvement in quality of life. Because of their pharmacokinetic and pharmacodynamic characteristics, rapid-action insulin analogues are imposed as best insulin to be used in CSII. The rapid onset and the fast reached peak make them better mimic the way how pancreas secretes insulin. CSII by pump is not free from issues. Catheter occlusions, blockages, clogs can arrest insulin administration. The consequent higher levels of glycemic values, can easily bring to the onset of ketoacidosis, with an high risk for patients' life. Aspart is a rapid analogue obtained by aminoacidic substitution. It is as effective as lispro and glulisine in gaining a good metabolic control and even better in reducing glucose variability. Some studies tried to compare rapid analogues in terms of stability. Obtained data are controversial. An in vivo study evidenced higher stability or glulisine, while studies in vitro highlighted a higher safety of aspart. Nowadays it is not possible to assess which analogues is safer. When the infusion set is changed every 48 hours equivalent rates of occlusions have been observed.
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Affiliation(s)
- D Pitocco
- Diabetes Care Unit, Agostino Gemelli Hospital, Università Cattolica, Rome, Italy -
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Pitocco D, Zaccardi F, Tarzia P, Milo M, Scavone G, Rizzo P, Pagliaccia F, Nerla R, Di Franco A, Manto A, Rocca B, Lanza GA, Crea F, Ghirlanda G. Metformin improves endothelial function in type 1 diabetic subjects: a pilot, placebo-controlled randomized study. Diabetes Obes Metab 2013; 15:427-31. [PMID: 23167274 DOI: 10.1111/dom.12041] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 10/09/2012] [Accepted: 11/13/2012] [Indexed: 01/07/2023]
Abstract
AIMS Several studies have investigated the effects of metformin treatment in patients with type 1 diabetes mellitus (T1DM). No study has hitherto examined its effects on endothelial function in these patients. In this study we sought to evaluate the effect of metformin on endothelial function in type 1 diabetic patients. METHODS Forty-two uncomplicated T1DM patients were randomized in a placebo-controlled, double-blind, 6-month trial to treatment with either metformin or placebo. Glycometabolic and clinical parameters as well as flow-mediated dilation (FMD) and nitrate-mediated dilation (NMD) of the right brachial artery were measured at baseline and at the end of the study. Glycaemic variability (GV, calculated from continuous glucose monitoring data) and a biomarker of oxidative stress [urinary 8-iso-prostaglandin F2α (PGF2α)] were also assessed. RESULTS Baseline data were similar in the two groups. Compared with placebo, metformin significantly reduced body weight [-2.27 kg (95% confidence interval: -3.99; -0.54); p = 0.012] whilst improved FMD [1.32% (0.30; 2.43); p = 0.013] and increased PGF2α [149 pg/mg creatinine (50; 248); p = 0.004]. Notably, the improvement of FMD did not correlate with the decrease of body weight (r(2) < 1%). NMD, haemoglobin A1c, GV, daily insulin dose and other parameters did not significantly change after the treatment comparing the two groups. CONCLUSIONS Our pilot trial showed that, in uncomplicated type 1 diabetic subjects, metformin improved FMD and increased PGF2α, a marker of oxidative stress, irrespective of its effects on glycaemic control and body weight. Randomized, blinded clinical trials are needed to evaluate the benefits and risks of metformin added to insulin in type 1 diabetes.
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Affiliation(s)
- D Pitocco
- Diabetes Care Unit, Department of Internal Medicine, Catholic University School of Medicine, Rome, Italy
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Abstract
Proteins and peptides fold into dynamic structures that access a broad functional landscape; however, designing artificial polypeptide systems is still a great challenge. Conversely, DNA engineering is now routinely used to build a wide variety of 2D and 3D nanostructures from hybridization based rules, and their functional diversity can be significantly expanded through site specific incorporation of the appropriate guest molecules. Here we demonstrate a new approach to rationally design 3D nucleic acid-amino acid complexes using peptide nucleic acid (PNA) to assemble peptides inside a 3D DNA nanocage. The PNA-peptides were found to bind to the preassembled DNA nanocage in 5-10 min at room temperature, and assembly could be performed in a stepwise fashion. Biophysical characterization of the DNA-PNA-peptide complex was performed using gel electrophoresis as well as steady state and time-resolved fluorescence spectroscopy. Based on these results we have developed a model for the arrangement of the PNA-peptides inside the DNA nanocage. This work demonstrates a flexible new approach to leverage rationally designed nucleic acid (DNA-PNA) nanoscaffolds to guide polypeptide engineering.
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Affiliation(s)
- Justin D Flory
- Center for Bio-Inspired Solar Fuel Production, Arizona State University, Tempe, Arizona 85287, United States
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Sizemore SM, Cope SM, Roy A, Ghirlanda G, Vaiana SM. Electrostatic Interactions Modulate the Structure and Dynamics of Calcitonin Gene-Related Peptide. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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